ArticleJournal of biomolecular NMR2007
Effects of side-chain orientation on the 13C chemical shifts of antiparallel beta-sheet model peptides.
Article in Journal of biomolecular NMR, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 31 citations in OpenAlex.
- Physics-based method to validate and repair flaws in protein structures.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- Protein backbone and sidechain torsion angles predicted from NMR chemical shifts using artificial neural networks.Journal of biomolecular NMR · 2013Article
- Improved chemical shift prediction by Rosetta conformational sampling.Journal of biomolecular NMR · 2012Article
- Density functional calculations of backbone 15N shielding tensors in beta-sheet and turn residues of protein G.Journal of biomolecular NMR · 2011Article
- β-Sheet 13C structuring shifts appear only at the H-bonded sites of hairpins.Journal of the American Chemical Society · 2011Article
- Sequential nearest-neighbor effects on computed 13Calpha chemical shifts.Journal of biomolecular NMR · 2010Article
- SPARTA+: a modest improvement in empirical NMR chemical shift prediction by means of an artificial neural network.Journal of biomolecular NMR · 2010Article
- Site-specific backbone amide (15)N chemical shift anisotropy tensors in a small protein from liquid crystal and cross-correlated relaxation measurements.Journal of the American Chemical Society · 2010Article
- Analysis of 13Calpha and 13Cbeta chemical shifts of cysteine and cystine residues in proteins: a quantum chemical approach.Journal of biomolecular NMR · 2010Article
- Assessing the accuracy of protein structures by quantum mechanical computations of 13C(alpha) chemical shifts.Accounts of chemical research · 2009Article
- Quantum-mechanics-derived 13Calpha chemical shift server (CheShift) for protein structure validation.Proceedings of the National Academy of Sciences of the United States of America · 2009Article
- TALOS+: a hybrid method for predicting protein backbone torsion angles from NMR chemical shifts.Journal of biomolecular NMR · 2009Article
- Performance of density functional models to reproduce observed (13)C(alpha) chemical shifts of proteins in solution.Journal of computational chemistry · 2009Article
- Quantum chemical 13C(alpha) chemical shift calculations for protein NMR structure determination, refinement, and validation.Proceedings of the National Academy of Sciences of the United States of America · 2008Article
- Dependence of amino acid side chain 13C shifts on dihedral angle: application to conformational analysis.Journal of the American Chemical Society · 2008Article
- Factors affecting the use of 13C(alpha) chemical shifts to determine, refine, and validate protein structures.Proteins · 2008Article
- Use of 13C(alpha) chemical shifts for accurate determination of beta-sheet structures in solution.Proceedings of the National Academy of Sciences of the United States of America · 2008Article
- Crystal polymorphism of protein GB1 examined by solid-state NMR spectroscopy and X-ray diffraction.The journal of physical chemistry. B · 2007Article
- Protein backbone chemical shifts predicted from searching a database for torsion angle and sequence homology.Journal of biomolecular NMR · 2007Article
- Predicting 13Calpha chemical shifts for validation of protein structures.Journal of biomolecular NMR · 2007Article
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Authors and funding
3 authors at 3 institutions in 2 countries.
Funding
Abstract
The dependence of the (13)C chemical shift on side-chain orientation was investigated at the density functional level for a two-strand antiparallel beta-sheet model peptide represented by the amino acid sequence Ac-(Ala)(3)-X-(Ala)(12)-NH(2) where X represents any of the 17 naturally occurring amino acids, i.e., not including alanine, glycine and proline. The dihedral angles adopted for the backbone were taken from, and fixed at, observed experimental values of an antiparallel beta-sheet. We carried out a cluster analysis of the ensembles of conformations generated by considering the side-chain dihedral angles for each residue X as variables, and use them to compute the (13)C chemical shifts at the density functional theory level. It is shown that the adoption of the locally-dense basis set approach for the quantum chemical calculations enabled us to reduce the length of the chemical-shift calculations while maintaining good accuracy of the results. For the 17 naturally occurring amino acids in an antiparallel beta-sheet, there is (i) good agreement between computed and observed (13)C(alpha) and (13)C(beta) chemical shifts, with correlation coefficients of 0.95 and 0.99, respectively; (ii) significant variability of the computed (13)C(alpha) and (13)C(beta) chemical shifts as a function of chi(1) for all amino acid residues except Ser; and (iii) a smaller, although significant, dependence of the computed (13)C(alpha) chemical shifts on chi(xi) (with xi > or = 2) compared to chi(1) for eleven out of seventeen residues. Our results suggest that predicted (13)C(alpha) and (13)C(beta) chemical shifts, based only on backbone (phi,psi) dihedral angles from high-resolution X-ray structure data or from NMR-derived models, may differ significantly from those observed in solution if the dihedral-angle preferences for the side chains are not taken into account.
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